Applications are open for the Bay Area RaMP 2023-24 cohort
Interested in a paid post-baccalaureate research training opportunity? Applications are now open for the Bay Area RaMP 2023-24 cohort.
Phylosymbiosis in Fish Microbiota
Despite the rapid diversification of morphology and behaviors among pupfish species, gut microbiota related much more closely to the phylogenies of their hosts than to their life history. Reported by the Martin lab (Integrative Biology) in PLOS ONE, September 16, 2022.
Probing Contaminated Environments
From the Terry group (Plant and Microbial Biology): Description of culture-dependent and culture-independent bacterial diversity in contaminated wastewater. Published in Journal of Environmental Management.
Nutrient Profiles Across Microbiomes
Cobamides are important nutrients in microbial communities that can act as public goods, so cobamide availability in a habitat might shape the structure of microbial interactions. New research from the Taga lab characterizes variation in cobamide composition across insect and mammalian guts and environmental samples. Published August 29, 2022 in Biochemistry.
Bouncing Back After Drought
A new study from the Taylor lab reports that soil fungi are generally more drought-resistant than bacteria, but also that drought disrupts intra- and inter-kingdom correlations in microbial co-occurrence networks. Published July 5, 2022 in Nature Communications.
Microbiome Method Development
Berkeley scientists contributed to two books this summer on characterizing the structure and importance of microbial communities. Learn how to properly run a microbiome GWAS in Methods in Molecular Biology, or read about soil microbiology in desert ecosystems in Microbiology of Hot Deserts. Congratulations to the Coleman-Derr and Northen groups!
Rewriting the Genetic Code
New work from the Banfield lab finds alternative stop codons are widely distributed among phage genomes, including in phages of human and animal gut microbiota. Stop codon has appeared repeatedly in closely related lineages, suggesting it can evolve rapidly. Published May 26, 2022 in Nature Microbiology.
Natural Product Discovery
New paper from the Traxler lab describes the discovery of a new family of antimicrobial compounds, referred to as the dynaplanins. The approach took advantage of natural patterns of antimicrobial production and resistance among soil actinomycetes. Published May 24, 2022 in mBio and selected as a 2022 Editor’s Pick.
The Chakraborty lab describes how strains within the genus Arthrobacter have adapted to a variety below-ground environments. Published March 30, 2022 in ISME Communications: https://doi.org/10.1038/s43705-022-00113-8
Core Taxa Respond to Fertilizer
The Koskella Lab describes how fertilizer alters the tomato rhizosphere microbiome. Published March 21, 2022 in Applied and Environmental Microbiology: https://doi.org/10.1128/aem.00049-22
The Rarefaction Debate
New work from the Fithian group reports a rarefaction efficiency index to determine the sensitivity of microbiome data to loss upon rarefaction and guide the decisions of researchers. Published February 25, 2022 in Bioinformatics: https://doi.org/10.1093/bioinformatics/btac127.
Single-Cell Sequencing Provides New Insights
The Joint Genome Institute demonstrates how single-cell sequencing reveals population structure in the microbial communities of hot springs. Published December 30, 2021 in ISME: https://doi.org/10.1093/femsec/fiab162.
The Rosenblum lab reports host and habitat influences on the microbial communities living on salamanders. Published December 16, 2021 in FEMS Microbiology Ecology: https://doi.org/10.1093/femsec/fiab162
Genome Editing in Communities
The Banfield and Doudna labs announce DART-ET-seq, a method for targeted DNA insertion in a community context. Published December 6, 2021 in Nature Microbiology: https://doi.org/10.1038/s41564-021-01014-7.
New Data Sharing Initiative
Announcement of the National Microbiome Data Collaborative Data Portal, a resource for hosting microbiome data that is accessible and usable across systems and studies: https://academic.oup.com/nar/article/50/D1/D828/6414581
New work from the Banfield Lab (Environmental Science, Policy, and Management) identifies traits of bacteria that help them to survive the infant gut. Published September 21st, 2021 in Cell Reports Medicine: https://doi.org/10.1016/j.xcrm.2021.100393
Better Together: CRAGE + CRISPR
The Yoshikuni group (Lawrence Berkeley Lab) integrates chassis-independent recombinase-assisted genome engineering with CRISPR to rapidly profile the function of bacterial biosynthetic gene clusters. Published September 10th, 2021 in Cell Chemical Biology: https://doi.org/10.1016/j.chembiol.2021.08.009
Microbial Arms Races
A multi-year study from the Koskella lab (Integrative Biology) describes co-evolutionary arms races between bacteria and phages in natural microbial communities. Published in The American Naturalist: https://doi.org/10.1086/717181
Fungi Around the World
A new study from the Dawson lab (Integrative Biology) analyzes biogeographic patterns of free-living and host-associated fungi. Read more in Ecology Letters: https://doi.org/10.1111/ele.13886
Adding Branches to the Tree of Life
Congratulations to the Banfield Lab (Environmental Science, Policy, and Management) for two new publications describing the diversity and metabolic capabilities of the largely uncultivated, ultra-small bacteria comprising the Candidate Phyla Radiation. Published July 13th, 2021 and August 17th, 2021 in mSystems: https://doi.org/10.1128/mBio.00521-21, https://doi.org/10.1128/mSystems.01205-20
Expanding Phage Collections
Nikos Kyrpides (Joint Genome Institute) and colleagues compiled a database of nearly 200,000 bacteriophage genomes and predicted protein clusters. Published June 24, 2021 in Nature Microbiology: https://doi.org/10.1038/s41564-021-00928-6
Iron Metabolism in Drought
Drought stress disrupts iron homeostasis in plant roots, leading to changes in root-associated microbial communities. Published by the Coleman-Derr lab (Plant and Microbial Biology) in Nature Communications, May 28, 2021: https://doi.org/10.1038/s41467-021-23553-7
Protists in the Microbiome
A large-scale field experiment from the Firestone lab (Environmental Science, Policy, and Management) shows that distinct protist communities inhabit the rhizosphere in different plant developmental stages, shedding new light on an understudied component of the plant microbiome. Published April 28, 2021 in Microbiome: https://doi.org/10.1186/s40168-021-01042-9
New Single-Cell Sequencing Pipeline
New pipeline developed by Jan-Feng Cheng (Joint Genome Institute) and colleagues for single-cell sequencing of microbial eukaryotes. Published April 23, 2021 in iScience: https://www.cell.com/iscience/pdf/S2589-0042(21)00258-3.pdf
New work from the Coleman-Derr lab (Plant and Microbial Biology) evaluated the contributions of polyploidy and domestication to wheat microbiome composition. Published March 18, 2021 in PLOS One: https://doi.org/10.1371/journal.pone.0248030